How to convert between different file formats
Question: I ran a query which gave me results in FASTA
format. Now I need to input the query results into an analytic tool that takes MSF format as input. What do I do?
Answer: You can use BioExtract Server's FormatConversion tool
to convert the query results into the format you need. This tool allows
conversion between many different formats. It can handle the conversion of a
single data sequence, as well as multiple data sequences. Here's how it works:
To input query results into the tool FormatConversion:
- Click the Tools tab. In the Available Tools list, click Edit Tools and select FormatConversion. The FormatConversion form opens in the right panel.
- In the Input Data section near the top of the form, select Use records on Extracts page formatted as FASTA. This tells the BioExtract Server to convert the query results listed on the Extracts page.
- In the Parameter Settings section, open the To Format drop-down menu. You'll see a variety of choices. Select the desired format.
- In the From Format drop-down menu, always choose fasta.
- Click the Execute button. Now wait until the status message displays "Execution complete!"
To verify that the conversion was successful:
- Once FormatConversion completes, open the Tool Results drop-down menu below the status message. You'll see two files: ReportFile.txt and result.txt.
- Open ReportFile.txt to see execution details. Open result.txt to see the converted results.
- Once you've verified that the conversion was successful, input the FormatConversion results into the tool you want to run.
To input the FormatConversion results into another tool:
- Click the Tools tab. In the Available Tools list, select the desired tool. Its form will open in the right panel.
- In the Input Data section near the top of the form, select Use previously executed tool results.
- Open the Select tool drop-down menu and select FormatConversion.
- Open the Select an output file drop-down menu and select result.txt.
- Complete the rest of the form according to your data and preferences, then click the Execute button. The tool begins to run with the FormatConversion file as its input.
Other important information
- If the FormatConversion tool can't handle what you need, add the web service tool
"seqret" to your account. Seqret allows conversion between many different
sequence file formats. Read Adding a Tool.